Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 315 bits (808), Expect = 1e-90 Identities = 188/381 (49%), Positives = 241/381 (63%), Gaps = 32/381 (8%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MATV+ K + Y K AV +D+ I DGEF+V VGPSGC KST+LRM+AGLED++GG Sbjct: 1 MATVSLRKIEKRYENGFK-AVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I IG+R V LPPKDR IAMVFQNYALYPH TV DNM F LK+ PK EI+++VE+AA Sbjct: 60 EIYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 + L++T+ L RKPK +SGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRVS R +IA Sbjct: 120 EKLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQ 179 Query: 181 LQRRL-----GITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGF 235 L R L T +YVTHDQ EA+T+GDR+ VL G + QVD+P ++Y+ P N FVA F Sbjct: 180 LHRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASF 239 Query: 236 IGSPAMNLVEVPITDGGVKFGNSVVPVNREALSAADKG-------DRTVTVGVRPEHFDV 288 IGSP++NL++ I + + P E L K ++ V G+RPEH Sbjct: 240 IGSPSINLIDTAIRKNNERLYVEIAP-GVEILIPHSKQVLLEGYINKPVCFGIRPEHI-- 296 Query: 289 VELGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQV 348 SL+ D D V + VVE +G++ ++Y VGG K+L+ RV+ + + Sbjct: 297 ---------SLASDDDDLNTFEGV-LTVVENMGSEKFLYFI--VGG--KELIARVDTQDI 342 Query: 349 P--EKGSTLHVVPRPGETHVF 367 G TL HVF Sbjct: 343 NPFHIGKTLRFNLNTAFCHVF 363 Lambda K H 0.317 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 377 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 376 Length adjustment: 30 Effective length of query: 347 Effective length of database: 346 Effective search space: 120062 Effective search space used: 120062 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory